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  1. IGB
  2. IGBF-3479

Make volcano plots from MvW results

        Details

        • Type: Task
        • Status: To-Do (View Workflow)
        • Priority: Major
        • Resolution: Unresolved
        • Affects Version/s: None
        • Fix Version/s: None
        • Labels:
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          Description

          Create a new markdown that take results from MvW-[assembly].txt and make volcano plots.

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              Task - A task that needs to be done. IGBF-3476 Find genes that differ between genotypes are and vf36 again

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                ann.loraine Ann Loraine added a comment - - edited

                Made a prototype RShiny app that reads results and makes a volcano plot. But it is not very good right now.
                It needs a way for users to select the comparison to show. Also, it puts all the SL4 and SL5 genes onto the same plot, which is weird.
                It might be better to show two plots - SL4 and SL5 next to each other.
                Finally, an RShiny app showing just one or two plots makes it difficult to quickly assess all the results. I bet it would be better to write a Markdown that creates all the plots and then just puts them into a multipage PDF, like we did with this paper ages ago: https://pubmed.ncbi.nlm.nih.gov/17369640/

                Unfortunately, however, I can't find the multi-page PDF *or* the code!

                Show
                ann.loraine Ann Loraine added a comment - - edited Made a prototype RShiny app that reads results and makes a volcano plot. But it is not very good right now. It needs a way for users to select the comparison to show. Also, it puts all the SL4 and SL5 genes onto the same plot, which is weird. It might be better to show two plots - SL4 and SL5 next to each other. Finally, an RShiny app showing just one or two plots makes it difficult to quickly assess all the results. I bet it would be better to write a Markdown that creates all the plots and then just puts them into a multipage PDF, like we did with this paper ages ago: https://pubmed.ncbi.nlm.nih.gov/17369640/ Unfortunately, however, I can't find the multi-page PDF * or * the code!
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                ann.loraine Ann Loraine added a comment -

                branch:

                https://bitbucket.org/aloraine/flavonoid-rnaseq/branch/IGBF-3479

                cc: [~molly]

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                ann.loraine Ann Loraine added a comment - branch: https://bitbucket.org/aloraine/flavonoid-rnaseq/branch/IGBF-3479 cc: [~molly]
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                ann.loraine Ann Loraine added a comment -

                More details on what this task involves:

                • Make a new Markdown that uses code from "DrawPlots.R" to create an HTML or PDF Markdown output file that shows volcano plots for every comparison shown in 72_F3H_PollenTube/results/MvW-SL4.txt and 72_F3H_PollenTube/results/MvW-SL5.txt
                Show
                ann.loraine Ann Loraine added a comment - More details on what this task involves: Make a new Markdown that uses code from "DrawPlots.R" to create an HTML or PDF Markdown output file that shows volcano plots for every comparison shown in 72_F3H_PollenTube/results/MvW-SL4.txt and 72_F3H_PollenTube/results/MvW-SL5.txt
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                ann.loraine Ann Loraine added a comment -

                Merged RShiny app code and new DrawPlots.R into main branch. Proceeding with new Markdown to create volcano plots in "bulk".

                Show
                ann.loraine Ann Loraine added a comment - Merged RShiny app code and new DrawPlots.R into main branch. Proceeding with new Markdown to create volcano plots in "bulk".

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                  • Assignee:
                    Unassigned
                    Reporter:
                    Mdavis4290 Molly Davis
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                    • Created:
                      Updated: